Announcing TPP version 4.0.0: windows native code and installer
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Joshua Tasman
Jun 4, 2008, 3:53:48 AM6/4/08
to spctools...@googlegroups.com, dont...@a.com, Ruedi Aebersold, Laurel Feltz
We are very pleased to announce the public release of TPP version 4.0.0 (jetstream). Version 4 introduces some major improvements and changes that all users should be aware of:
* The TPP executable programs are now build as native Windows. All programs should see some speed increases-- some quite substantial. Our thanks to Insilicos for donating their windows optimizations from the IPP project and adding support to make the TPP buildable under mingw.
* The TPP cygwin distribution will be retired: the native windows systems does not require cygwin (the unix emulation layer for windows.) This should remove many installation and configuration issues for users and developers. Cygwin releases will follow mingw for the 4.0.x series to allow people to continue to use TPP without disrupting their existing workflows, but the mingw distribution is recommended and will be the focus for support. The cygwin release will follow shortly.
*mzML support: all TPP programs should be able to use the new format, developed by a collaboration between HUPO-PSI, SPC, vendors, and others.
*SPC converters no longer require support files (zlib and the Microsoft C++ redistributables); these are included (statically linked) in the executables. Please note that wolf.exe has been renamed to massWolf.exe to avoid any confusion.
* windows installer: The TPP 4.0 installer is a native windows program. This installer will configure and install a webserver, if necessary, as well as the Perl language. The entire TPP installation is included in one file. This is a typical windows installer, which can be easily uninstalled through the typical Windows Control Panel (Add/Remove Programs).
As this represents a large change for the TPP, there are undoubtedly some rough edges remaining, we decided that the many benefits to this new version outweigh any downsides of the change.
*known issues and important notes*
- older TPP cygwin versions are strongly recommened to be completely removed from the system, by exactly following the instructions here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Windows_Cygwin_Installation#Uninstalling_the_TPP
- if C:\Inetpub was created by cygwin before native installation, you may get an installation error in which the webserver does not start. We are aware of this and are trying to track it down. In the meanwhile, a workaround is to move your data out of C:\Inetput\wwwroot, along with any other custom scripts, programs, or data; remove C:\Inetpub completely, rerun the native 4.0.0 installer, and reboot. Then, replace your data files.
- some 0-byte tempfiles may be left in the WEBSERVER_TMP directory (C:\tmp)
- currently qualscore may not run unless you manually configure your java CLASSPATH environmental variables.
Download the TPP version 4.0.0 native windows installer (TPP_Setup_v4_0_JETSTREAM_rev_0.exe) from the Sashimi SourceForge project file release page:
http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912
Special thanks to:
Brian Pratt at Insilicos for the majority of the native windows conversion and optimization and the windows installer
Darren Kessner and Matt Chambers for their work on mzML support and conversion with the PWIZ project (http://proteowizard.sourceforge.net/)
And all other TPP developers and beta testers.
For downloading and installing the Windows cygwin version (when available) please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-0-0
Please refer to the readme file in TPP/src as well as the wiki.
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
The SPC Tools Team: Josh, Luis, and David
* The TPP executable programs are now build as native Windows. All programs should see some speed increases-- some quite substantial. Our thanks to Insilicos for donating their windows optimizations from the IPP project and adding support to make the TPP buildable under mingw.
* The TPP cygwin distribution will be retired: the native windows systems does not require cygwin (the unix emulation layer for windows.) This should remove many installation and configuration issues for users and developers. Cygwin releases will follow mingw for the 4.0.x series to allow people to continue to use TPP without disrupting their existing workflows, but the mingw distribution is recommended and will be the focus for support. The cygwin release will follow shortly.
*mzML support: all TPP programs should be able to use the new format, developed by a collaboration between HUPO-PSI, SPC, vendors, and others.
*SPC converters no longer require support files (zlib and the Microsoft C++ redistributables); these are included (statically linked) in the executables. Please note that wolf.exe has been renamed to massWolf.exe to avoid any confusion.
* windows installer: The TPP 4.0 installer is a native windows program. This installer will configure and install a webserver, if necessary, as well as the Perl language. The entire TPP installation is included in one file. This is a typical windows installer, which can be easily uninstalled through the typical Windows Control Panel (Add/Remove Programs).
As this represents a large change for the TPP, there are undoubtedly some rough edges remaining, we decided that the many benefits to this new version outweigh any downsides of the change.
*known issues and important notes*
- older TPP cygwin versions are strongly recommened to be completely removed from the system, by exactly following the instructions here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Windows_Cygwin_Installation#Uninstalling_the_TPP
- if C:\Inetpub was created by cygwin before native installation, you may get an installation error in which the webserver does not start. We are aware of this and are trying to track it down. In the meanwhile, a workaround is to move your data out of C:\Inetput\wwwroot, along with any other custom scripts, programs, or data; remove C:\Inetpub completely, rerun the native 4.0.0 installer, and reboot. Then, replace your data files.
- some 0-byte tempfiles may be left in the WEBSERVER_TMP directory (C:\tmp)
- currently qualscore may not run unless you manually configure your java CLASSPATH environmental variables.
Download the TPP version 4.0.0 native windows installer (TPP_Setup_v4_0_JETSTREAM_rev_0.exe) from the Sashimi SourceForge project file release page:
http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912
Special thanks to:
Brian Pratt at Insilicos for the majority of the native windows conversion and optimization and the windows installer
Darren Kessner and Matt Chambers for their work on mzML support and conversion with the PWIZ project (http://proteowizard.sourceforge.net/)
And all other TPP developers and beta testers.
For downloading and installing the Windows cygwin version (when available) please visit the
following guide on our wiki:
"http://tools.proteomecenter.org/wiki/index.php?title=TPP:User_Documentation"
For downloading the source code, please go to the following link:
"http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912"
or directly from svn: see
http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-0-0
Please refer to the readme file in TPP/src as well as the wiki.
Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
The SPC Tools Team: Josh, Luis, and David
Joshua Tasman
Jun 4, 2008, 3:54:42 AM6/4/08
to spctools...@googlegroups.com, dont...@a.com, Ruedi Aebersold, Laurel Feltz
We are very pleased to announce the public release of TPP version 4.0.0 (jetstream). Version 4 introduces some major improvements and changes that all users should be aware of:
* The TPP executable programs are now build as native Windows. All programs should see some speed increases-- some quite substantial. Our thanks to Insilicos for donating their windows optimizations from the IPP project and adding support to make the TPP buildable under mingw.
* The TPP cygwin distribution will be retired: the native windows systems does not require cygwin (the unix emulation layer for windows.) This should remove many installation and configuration issues for users and developers. Cygwin releases will follow mingw for the 4.0.x series to allow people to continue to use TPP without disrupting their existing workflows, but the mingw distribution is recommended and will be the focus for support. The cygwin release will follow shortly.
*mzML support: all TPP programs should be able to use the new format, developed by a collaboration between HUPO-PSI, SPC, vendors, and others.
*SPC converters no longer require support files (zlib and the Microsoft C++ redistributables); these are included (statically linked) in the executables. Please note that wolf.exe has been renamed to massWolf.exe to avoid any confusion.
* windows installer: The TPP 4.0 installer is a native windows program. This installer will configure and install a webserver, if necessary, as well as the Perl language. The entire TPP installation is included in one file. This is a typical windows installer, which can be easily uninstalled through the typical Windows Control Panel (Add/Remove Programs).
As this represents a large change for the TPP, there are undoubtedly some rough edges remaining, we decided that the many benefits to this new version outweigh any downsides of the change.
*known issues and important notes*
- older TPP cygwin versions are strongly recommened to be completely removed from the system, by exactly following the instructions here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Windows_Cygwin_Installation#Uninstalling_the_TPP
- if C:\Inetpub was created by cygwin before native installation, you may get an installation error in which the webserver does not start. We are aware of this and are trying to track it down. In the meanwhile, a workaround is to move your data out of C:\Inetput\wwwroot, along with any other custom scripts, programs, or data; remove C:\Inetpub completely, rerun the native 4.0.0 installer, and reboot. Then, replace your data files.
- some 0-byte tempfiles may be left in the WEBSERVER_TMP directory (C:\tmp)
- currently qualscore may not run unless you manually configure your java CLASSPATH environmental variables.
Download the TPP version 4.0.0 native windows installer from the Sashimi SourceForge project file:* The TPP executable programs are now build as native Windows. All programs should see some speed increases-- some quite substantial. Our thanks to Insilicos for donating their windows optimizations from the IPP project and adding support to make the TPP buildable under mingw.
* The TPP cygwin distribution will be retired: the native windows systems does not require cygwin (the unix emulation layer for windows.) This should remove many installation and configuration issues for users and developers. Cygwin releases will follow mingw for the 4.0.x series to allow people to continue to use TPP without disrupting their existing workflows, but the mingw distribution is recommended and will be the focus for support. The cygwin release will follow shortly.
*mzML support: all TPP programs should be able to use the new format, developed by a collaboration between HUPO-PSI, SPC, vendors, and others.
*SPC converters no longer require support files (zlib and the Microsoft C++ redistributables); these are included (statically linked) in the executables. Please note that wolf.exe has been renamed to massWolf.exe to avoid any confusion.
* windows installer: The TPP 4.0 installer is a native windows program. This installer will configure and install a webserver, if necessary, as well as the Perl language. The entire TPP installation is included in one file. This is a typical windows installer, which can be easily uninstalled through the typical Windows Control Panel (Add/Remove Programs).
As this represents a large change for the TPP, there are undoubtedly some rough edges remaining, we decided that the many benefits to this new version outweigh any downsides of the change.
*known issues and important notes*
- older TPP cygwin versions are strongly recommened to be completely removed from the system, by exactly following the instructions here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Windows_Cygwin_Installation#Uninstalling_the_TPP
- if C:\Inetpub was created by cygwin before native installation, you may get an installation error in which the webserver does not start. We are aware of this and are trying to track it down. In the meanwhile, a workaround is to move your data out of C:\Inetput\wwwroot, along with any other custom scripts, programs, or data; remove C:\Inetpub completely, rerun the native 4.0.0 installer, and reboot. Then, replace your data files.
- some 0-byte tempfiles may be left in the WEBSERVER_TMP directory (C:\tmp)
- currently qualscore may not run unless you manually configure your java CLASSPATH environmental variables.
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